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I have two polygon shapefiles, one is county boundaries and the other is the National Flood Hazard Layer that shows areas in the floodplain. The flood layer is an extremely complex and challenging file to work with. It has many polygons that have 1 million + vertices and many overlapping polygons (that shouldn't be).

My goal is to find the area of counties either covered by the floodplain polygons or the area that is not covered by the polygons. Here's what I've done so far...

I first tried using identity to and then summary statistics on the county and flood layer. Unfortunately because there are so many overlapping polygons my output is wildly inaccurate sometimes with more than 100% of the county being covered by floodplain.

I then tried using topology with the polygons must not overlap tool and the create feature error fix. Unfortunately this crashes arcmap every time I run it.

My next thought was to calculate the area not covered by any polygon hence bypassing the problem of overlapping polygons. I'm currently trying to turn the polygon shapefile into a raster to do this but its a slow process.

I have computers running ArcMap 10.2.2 and 10.3 with advanced licences.

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First back up your flood layer (save a backup file), then start editing it and use the merge tool to merge all the features in your flood layer. If the flood layer has many overlapping features, it is best to merge a few features at a time until you only have one row in the attribute table).

Once you have a merged flood layer, you can use intersect or spatial join with the county layer to easily mark areas covered by the flood layer.

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I ended up using erase (not sure why I didn't think of it before) and removing all the flood zones from the county polygon, which got me the area not in the flood zone.

I also started to do what yanes suggested and I think this would have been the best route had I wanted to keep the flood layer.

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